After the Siege
by finnstardust
Summary: After Atlantis survives the Wraith attack, John and Elizabeth's relationship changes.


Well, here is a first attempt at Atlantis fanfic. It's John/Liz as I'm a major fan of that pairing. Reviews welcomed, good and bad. Hope you enjoy!

Disclaimer: I don't own anything to do with Stargate Atlantis. Sadly.

Spoilers: The Siege Part III

* * *

That night, darkness fell over Atlantis like it had done on every night previously, moon rose to shine like it always did. Outside, nothing seemed different but on the inside, the chaos caused by the Wraith attack was still being sorted out, defences checked frantically even though the cloaking of the city had seemed to fool their enemy for now. 

John Sheppard had retired from the control room a couple of hours previously, wanting nothing more than to sink into bed and sleep until awaken by the next mission or unscheduled gate activation; now that he was in his room, however, all attempts at sleep evaded him. Giving up, he picked up the copy of War and Peace, still unfinished, and found the spot he had got to before this mayhem had started. A part of him wondered at the fact that he was actually here to continue reading because, all things considered, he should be dead right now.

A knock on the door interrupted John just as he was getting up to speed again and he groaned, glancing at his watch. It was late, very late.

"Come in."

The door slid open with the familiar soft sound and he blinked at the woman standing on the doorway.

Elizabeth Weir looked like he would expect her to look in this situation; tiredness pressing heavily on her entire body, her eyes shadowed by dark circles which made his jaw clench, but what worried him the most was the expression in her eyes. Drawn, sad, hesitant and so horribly tired. For all the time he had known her during this expedition, she had never allowed her tiredness or her feelings to show, giving everyone else a part of her strength in the process.

He sat up on the bed. "Elizabeth."

She gave a tired smile. "I'm sorry to bother you this late, John, although I did expect to find you asleep…"

He glanced at the book in his hand. "I couldn't sleep."

She nodded, taking a few steps into his room. "I understand. I guess narrowly escaping death on a suicide mission tends to do that to you, not that I have any experience."

John chuckled. "Me neither. Not until today."

"Right. Anyway, I'm here because Caldwell insisted I wake you up to look at these. I tried to insist they could wait until tomorrow but…" She raised a bunch of papers in her hand and he detected a hint of coldness in her voice at the name of the colonel. He didn't blame her; the new military presence was slightly unsettling.

"It's tomorrow already", he indicated with a nod towards the clock on his nightstand. "What are they?"

"New security plans." She handed him the papers and he noticed her swaying a little.

"Looks good."

She frowned. "John, you haven't even…"

"If he thinks I'm going to get up in the middle of the night to look at some theoretical drawings which are of no use to us at the moment, he has another thing coming", he scowled. "You should realize that."

She looked away, tired. "He has a right to interfere with how the city is run, unfortunately."

"That does not include denying people their sleep", he cut in. "Especially after a day like this."

"I guess." She took the papers from him and walked to the door. "I'll tell him you accept…"

"Hold on, you're not telling him anything. Not tonight, anyway. Elizabeth, you need to sleep."

She gave a tight smile over her shoulder. "I do wish I had time for that luxury. Good night, John."

"Liz…"

She stopped on her tracks and bowed her head for a moment, before turning back. "What?"

"Dr. Weir may not need sleep but you do. Elizabeth does."

Her jaw clenched. "What is this, some Jekyll and Hyde personality clash? And I have not given you permission to call me Liz."  
"I didn't know I needed permission…Doctor."

His voice had turned cold, she realized, and arguing with him was the last thing she needed right now.

"I have to go." She turned around again but a wave of dizziness washed over her and she had to grasp the doorframe to stay upright. John was out of bed in a flash, practically dragging her back to the room and pushing her down to sit on the bed.

"What about when you faint, Elizabeth? Will that be enough to convince you to rest? Because I can get Carson to take you straight to the infirmary and there's nothing you or Caldwell can say about it."

"I'm fine, John." She tried to get up but he pressed down her shoulders.

"You're not going anywhere."

He walked to close the door and locked it for good measure.

"What are you doing? John…"

"I don't trust you to not do any work or actually sleep in your own quarters so you're sleeping here." He grabbed her leg and started to pull off her boots.

"I can't sleep here." She struggled but tiredness rendered it somewhat futile.

"Well, you're going to try." He had gotten her boots and socks off and pushed her down on the bed.

"I didn't mean that. I meant…if somebody finds out…"

"Yeah and then what?" He scowled. "I doubt it would much increase the amount of rumours that are already going around."

"What rumours? John, what are you talking about?" Elizabeth sat straight up.

He assessed the temperature of the room and pulled off her jacket, deciding she would be warm enough to sleep in her grey shirt before another thought told him she had probably been wearing it for days.

He pushed her back down. "You haven't heard? Most of them are about me and Teyla though."

She frowned. "Yeah, I know of those. But me and you?"

A smile tugged on the corner of her mouth and he couldn't help a smile of his own. "A ridiculous thought, right?"

She yawned and said nothing.

He got up to pull out a t-shirt from his closet. "Here. I won't look."

"But I'm not going to…"

John shot her a warning look. "Yes, you are."

Some more reasons why she really shouldn't be doing this surfaced in her mind but she really was very, very tired. And the bed felt so nice and inviting under her. "Fine."

She started pulling off her shirt and he turned away, walking to the door and listening to any sounds from outside. He heard nothing; this part of the city seemed to be in deep sleep.

"Caldwell is going to kill me", he heard her mutter. "Probably several times."

He chuckled. "Even for you, Elizabeth, that's impossible."

She arranged her clothes on the chair next to his bed. "I somehow doubt it."

He took a glance at her and noticed she looked very nice in his black shirt; dark curls a mess, long legs bare up to mid-thigh before she swung them under the covers, positioning herself gingerly on the other side of the bed.

"These beds were obviously not designed for sharing", she muttered, eyes closed.

"Oh, I wasn't going to…"

"John." She injected a dose of steel into her voice. "If you're forcing me to sleep here, I'm certainly not going to do it alone."

He smiled briefly. "Right."

Moving to grab War and Peace and marking the page he'd got to with a tiny fold of the corner, he placed the book back on the nightstand and positioned himself next to Elizabeth, willing the lights to dim on their own. She was right; there wasn't much space between them and he was thankfully too tired to start thinking about the fact that he was sharing a bed with his boss.

* * *

John awoke a few hours later with a start, forcing the haunting images of enemy ships and Wraiths out of his head. It was pitch dark and very quiet. A glance at the clock told him it was also very early, or late, whichever way you chose to look at it. 

Gradually he became aware of someone else next to him and remembered forcing Elizabeth to get some sleep in his bed. She had snuggled closer in her sleep, her head on his shoulder, her hand on his chest. He chuckled, thinking how she would vehemently deny all of it in the morning, being a very private and independent person. His eyes used to the darkness enough; he took a look at her face, peaceful and relaxed in deep sleep, only the slight furrow of her brow telling him she hadn't let go completely of whatever horrors she had experienced during the past few days. He remembered the long look they had shared before he had left for the suicide mission; for some reason he had got stuck into her eyes, the desperation and worry in them, the realization that if this worked, they would never see each other again. He remembered the hug she had given him when he had returned against all odds, holding him for a long time, the emotions in her eyes clearly visible as she pulled back, perhaps for the first time revealing anything of her soul. He felt like he had finally got close to Elizabeth herself at that moment, through the Dr. Weir defences and walls she had around her. As quick as it had come, however, the moment was over and she was back to full professionalism again. The hug had knocked him out of balance somewhat; she wasn't known to touch anybody, certainly not like that and he suspected she had seen it coming even less than he had.

She moved and mumbled something in her sleep and he lifted a hand to smooth some hair from her forehead, attempting to calm her down back to deep sleep. For a moment he thought he'd succeeded until her eyes fluttered open briefly, finding his in the darkness of the room.

He was fully prepared for her to startle and shoot as far away from him as was possible in the narrow bed but Elizabeth shocked the hell out of him by snuggling even closer, hiding her face between his jaw and neck.

"John…I thought you were dead."

The words were whispered so softly and quietly he barely heard them but they stunned him nevertheless. Moving his head so that he could press his lips against her hair, scented with the faint trace of strawberry from her shampoo, he wrapped his arms around her shoulders.

"I didn't. I'm fine and so are you. Everybody is."

She let out a sound that he deciphered as a slight sob. "Ford…"

John sighed, wishing she wouldn't worry about the young lieutenant right now, not when she so desperately needed to sleep.

"I know. But we'll find him. I'm sure of that."

Elizabeth hid her face even deeper and he could feel her body relaxing in sleep once again. "Promise?"

"I promise." The words came out easily no matter how false they may have been; they both knew finding Ford would not be easy and, in this situation, nothing was certain. She had tried to do the same earlier, to convince him they would succeed in tracking Ford down and he had believed her, at least to some extent. It was another reminder of how convincing she could be, even if she didn't really believe her own words.

* * *

Elizabeth woke up alone, in a room that was not hers. She stared around for a while before the events of the previous evening flooded back to her. Raising herself to lean on her elbows she scanned the room: John was nowhere to be seen but she could hear the faint sounds of shower running in the bathroom. 

She yawned, surprised at how much better she felt after just one night of deep sleep. For seven blissful hours she had been granted relief from the ever-present worries and things that needed to be done to keep Atlantis running: now they were back on her mind and she sighed, hoping that for just one day she could wake up in the morning in the amazing state of having nothing to worry about.

John stepped out of the bathroom, wearing a navy blue bathrobe. "Morning."

"Morning", she replied with a slight smile. "Where'd you steal that from?"

"Me, steal?" He feigned innocence. "It's mine, honestly bought."

"Right."

"You don't believe me", he said, like it was an obvious fact. "How are you feeling?"

"A lot better. Thank you, John, for doing what you did. I really needed sleep."

"I know." He flashed her his irresistible 'I-was-right-after-all' grin and she rolled her eyes.

"Now if I can only get out of here without anybody noticing, I'm all set for Caldwell to shout at my face."

"He won't. You did nothing wrong."

Elizabeth groaned, climbing out of bed and John's eyes travelled back down her legs again as she walked to the bathroom. "Hungry?"

"Starving." She smiled. "I guess I have forgotten to eat as well as to sleep."

"I guess so." He got dressed and waited for her to come out of the bathroom. She pulled on her pants but still stuck to his shirt while he peeked out of the room to check the corridor.

"All clear." Their rooms were almost next to each other so she should make the distance without much trouble.

"I'll see you at the mess hall for breakfast", he said as she ducked into her room. She opened her mouth to object but he was faster. "No buts. You have to eat."  
Elizabeth rolled her eyes. "Fine. I'll see you there."

"Oh and by the way", he said as the door was about to close.

"Yes?"  
"Now can I call you Liz?"

A brief stint of annoyance brushed her face but she couldn't help but smile at his lost puppy expression.

"Oh all right then. But don't you dare to do it in front of anyone, especially McKay. I'd never live it down.

"Right. I'll be sure to limit it to…private moments." He flashed her another grin and turned on his heels, heading to the mess hall. She looked after him for a long moment, shaking her head. Impossible man.

* * *

"We needed you last night, Dr. Weir. It was very unprofessional of you to just disappear like that.""I told you, I needed sleep. I wouldn't have been much good to you half-dead." 

Elizabeth tried her best to keep her voice at an even level and not shout at Colonel Caldwell like she really wanted to. The great feeling brought on by good night's sleep, two cups of coffee and a substantial breakfast was dissolving and fast.

"Fine. But in the future I want you to tell me exactly when you're planning little stunts like these."  
She swallowed back an angry reply. "Certainly, Sir."

"Did you show the security plans to Major Sheppard?"

"Yes. He approved of them but I think he'll want to go over them in more detail this morning, if you don't mind."

"That's fine. In the meantime, I'll go give Zelenka and McKay instructions; they can start thinking about how to realize the plans."  
He left the office and Elizabeth released the breath she had been holding. What a complete bastard!

John entered through the open door, security plans on hand. "What did Mr. Sunshine say?"

She smiled; his presence was like an injection that instantly made her feel better. "A lot. I can't remember any of it now, though."

"Good. Listen, we need to talk about Ford."

Elizabeth's face clouded over and he hated to be the one to cause that. "I know it's not easy but we need to draw up a plan to find him."

"I know, I just…" she rubbed her face wearily. "I don't know where to start."

"I think we should assemble teams, go to mainland to ask if they have any ideas or could offer any help."

She sighed. "God, John, how long have we been out here? Less than a year? And look at everything that's happened already. How much more can we take before it's too much?"

He wondered for a moment what had brought out this more pessimistic and reflecting side to her; not that he himself was on any better mood but Elizabeth was usually able to see clearly in any situation.

"Don't think about that, Liz. Don't give up on us. We need your strength."

She glanced around briefly, as if to check if there was anyone in the room who shouldn't hear him calling her Liz, then gave a tired half-smile. "I'm not giving up. It's just that sometimes…sometimes this gets too much."

"I know." He reached out a hand to squeeze her arm gently. "But we'll get through it. We've gotten through so much already."

She nodded, taking a moment to collect herself and to slip the Dr. Weir façade back on.

"Right. What are your plans?"

* * *

Later, she watched from the control room as John's newly assembled teams slipped through the Stargate, each heading for a separate friendly planet to ask for help in finding Ford. To her enormous relief, Colonel Caldwell had insisted on going with John and although she felt sorry for the Major having to deal with him for the day, she was happy for herself for even brief moments of peace. 

Leaving Zelenka temporarily responsible for the control room Elizabeth wandered around Atlantis for a couple of hours, just thinking, sometimes stopping to check in with a member of the personnel, to make sure they were all right. Somehow her journey took her back to the living quarters and she found herself standing in front of John's door.

Lifting her hand to caress the wooden frame, her fingers instinctively found their way to the panel next to it and before she knew it, had entered his code to get the door open. As the ranking leaders of this expedition, they knew each other's codes by heart.

The door swished open and her eyes fell on the bed she'd spent last night on. A brief smile crossed her lips as she remembered how adamant he had been to not let her out of the room, to force her to get some sleep. If it had been anyone else, she would probably have reprimanded them for inappropriate behaviour but John had a special way of getting his way with her. She didn't want to think about why that was.

Walking forward, she sat on the bed and the door closed behind her. She knew that if anyone caught her going in or coming out from her second-in command's living quarters, they would never live the rumours down. She sighed, closing her eyes for a moment and enjoying the feel of the soft bed against her weary body. She didn't remember much of last night, but a vague memory of waking up in the middle of the night plagued her. She knew that at some point of the night she had been very close to John, thoroughly enjoying his strong, warm body next to her, as close as they could get without…

Elizabeth drew in a shaky breath and shook her head; this was not the right time to start wondering about things like this, certainly not to start getting any ideas into her head about what might be going on between her and John. As far as she knew, he only saw her as his boss and possibly a friend but last night had definitely shifted something in their relationship, making them much closer than before. She had always found him tremendously attractive, even too much so for his own good. He was the only one here who had got through her defences, who made her laugh for real reasons, not just for professional jokes like Rodney or Carson. She knew how easy it would be to let herself fall in love with him, after all, most of the other female expedition members already were, and that was exactly why she needed to keep her head straight about this. It might seriously undermine their leaderships, especially with the presence of Colonel Caldwell. She knew a lot of people were certain he was sleeping with Teyla; the betting polls about John and herself had been news to her.

Her earpiece crashed. "Dr. Weir?"

"Yes?"

"Major Sheppard just radioed in; they've found some people who might be able to help with finding Ford. He wanted to know if he could bring them back to Atlantis."

Elizabeth thought for a moment. "What do we know about them?"

"They're our allies, or at least have professed to be. Teyla says we can trust them, Caldwell isn't so sure."

She knew how dangerous it might turn out if they brought in people who could potentially turn out as enemies. "I'm not sure. Give me a minute to get there; I want to talk to the team myself."

She took one last look at the bed and slipped out of the door.

* * *

In the end, she allowed John's team to bring back a few people from the planet they had travelled to, after determining their intentions were indeed friendly. Talks and negotiations proved somewhat useful but as the visitors stepped back through the Stargate, they weren't really any closer to finding Lieutenant Ford. 

Elizabeth rubbed her tired face. "Now what?"  
Caldwell drummed the table with his fingers, adding to her headache. "We keep searching. Keep in mind this was only one planet. In the meantime, I'll go see how the scientists are getting on with the security plans."

The door swung shut behind him and John glanced at the woman sitting by the table, fingering the laptop cover. "Are you all right?"

"Hmm", she replied, absent-mindedly before looking up at him. "I'm sorry, John, what did you say?"

"I asked if you were all right." He swung his body up from the seat and walked to stand behind her. She tilted her head up to keep eye-contact. "What are you doing?"

"Just relax."

He lowered his hands on her shoulders, gently starting to massage them and she couldn't help a moan escaping her throat.

"God, that feels amazing."

He chuckled softly. "I know."

Elizabeth scoffed. "Full of yourself much?"

"No, I just happen to have faith in my skills as a masseur." He moved his hands upwards to her neck, rubbing away the tension gathered during the last few days, if not months. Elizabeth lowered her head, eyes closed, nearly falling asleep.

"Well, I have to say that this time I agree."

He smirked. "This time only?"

"Don't push your luck, Major."

"Wouldn't dream of it, Doctor." He abandoned her neck and pushed his hands into her hair, gently pulling and tugging at the dark curls until she was sure she'd died and gone to heaven. She remembered her mother giving her head rubs when she had been a child; it had been the best moment of the day but after that she hadn't found anyone willing to carry on. Picking John Sheppard for this expedition seemed to pay off really handsomely.

"Liz?" His strong fingers concentrated on her scalp. "Are you sleeping?"

"Uh-huh." Her eyelids were severely drooping; if he only went on a little bit longer...

Then fingers were withdrawn from her hair.

"John?" She protested quietly but he had already circled the table.

"Not too much of a good thing", he grinned and she barely resisted the urge to throw a book or worse, her laptop at him. "Besides it's dinner time, come on."

"I can't…" Her answer was automatic before she even thought about it.

"Yes, you can. I'll bet you Caldwell is already there anyway. Even if I don't like him, at least he remembers to eat."

Elizabeth rolled her eyes but knew he was right; there was nothing else they could do at the moment.

* * *

That night, John wasn't really surprised to hear a knock on his door as he was getting ready to go to bed. He let her in without any questions, turning down bedcovers and watching as she placed herself onto his bed, so naturally it was like she had been sleeping here forever. 

"Thank you", she whispered softly, snuggling close to him, head on his shoulder. He only gave her a gentle smile, wishing good night and willing the lights to dim, just before falling asleep registering she was wearing his t-shirt again.


End file.
